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Great point. The units are not zoned but at the same time there is nothing that prevents tenants from closing
off their vents and thereby restricting airflow.

If you're concerned about the lowered airflow not evenly heating your home or getting to all of the rooms, I would say that rather you'll experience a quieter, lower static system in low stage (where it will spend a large portion of its time) that will provide even comfort. Of course this hinges on the adequacy of your duct design and we can't see it from here (beyond what you've told/shown us). 2-stage systems are for comfort, and most do decrease airflow in low stage to maintain temperature rise.

Can't add much to what's been said. Curious though. What mdl thermostat was installed? This furnace for optimal operation works best in a true 2 stage thermostat that controls heating stages not a timer on control board.

I sympathize with your situation, but not much of the attitude you have displayed here. Please don't think that you can discern what is required to select and implement a properly designed HVAC system by reading a manual or sales literature, or even with the advice you get here. When you see is only a thin veneer of what is required to make a system run the way it should. As a quick example of that, because of our altitude, the BTU output of the furnace is lower, but at the same time, we also need to move more air for best efficiency of the heating and cooling systems. Confusing, huh?

Another example would be the use of the nest. For the money there are much better choices.

You mentioned the ducts being covered by the manual J. Manual J doesn't cover ducts. That's different. And I wouldn't trust a company to do a manual J, if they don't do them as a routine part of their install procedure. That's a huge red flag. One more thing. If the manual J came up with 60,000 BTU's heating requirement, you would never use a 60,000 BTU furnace unless you or your tenants had a high tolerance for temperature dips in winter, or you planed on upgrades to the building's thermal envelope.

Stop putting the cart before the horse. I'm appalled, but not surprised at the number of hack-job mistakes that have apparently been committed at your residence. A big ad in the phone book does not equate to technical competence.

What lies behind us and what lies before us are small matters compared to what lies within us.

I sympathize with your situation, but not much of the attitude you have displayed here. Please don't think that you can discern what is required to select and implement a properly designed HVAC system by reading a manual or sales literature, or even with the advice you get here. When you see is only a thin veneer of what is required to make a system run the way it should. As a quick example of that, because of our altitude, the BTU output of the furnace is lower, but at the same time, we also need to move more air for best efficiency of the heating and cooling systems. Confusing, huh?

Another example would be the use of the nest. For the money there are much better choices.

You mentioned the ducts being covered by the manual J. Manual J doesn't cover ducts. That's different. And I wouldn't trust a company to do a manual J, if they don't do them as a routine part of their install procedure. That's a huge red flag. One more thing. If the manual J came up with 60,000 BTU's heating requirement, you would never use a 60,000 BTU furnace unless you or your tenants had a high tolerance for temperature dips in winter, or you planed on upgrades to the building's thermal envelope.

Stop putting the cart before the horse. I'm appalled, but not surprised at the number of hack-job mistakes that have apparently been committed at your residence. A big ad in the phone book does not equate to technical competence.

I'm stuck with the company that did the install so I have to work thru it. The number of hack jobs is ONE. The wrong equipment and initial single return air added to level 2. Red flags don't matter at this point as you say. I am committed to working thru it. There are a few people that have added value here. But not many. Believe me I am not using this forum or sale literature for the only input. I had many bids from large companies prior to selecting. I believe this "industry" is very full of people who just want to get in the door then start the discovery process. I am holding this companies feet to the fire. They WILL replace the equipment. The person that made the sale is now fired due to improper sizing. Whatever you call the duct sizing if it is not included in the manual J. It is done. You may not like the nest but you do not know all my requirements. the ability co control it remotely, get reports, lock and adjust it remotely get future updates etc are all part of my requirements. If you have another please recommend rather than complaining there are better then walk away without providing model numbers or recommendations, The property is an hour away. I need ability to change fro heating to cooling and remote management and locking.

Given altitude and heat load I am really really down to considerations for the two 75K BTU two stage furnaces. I am only seeking input for considerations as I approach this next week. That is all.

I don't understand why I wouldn't pick the furnace size without accommodations. The redone calculation says I need a 75K BTU furnace. I don't want to install larger than that. Since there is one thermostat I plan to lock it electronically and maintain a constant temp to the greatest extent possible.